An overview of apple rootstock development and selection

1. Concepts of Apple Rootstock
Breeding and Selection:
A Journey Through the
Development of New Apple
Rootstocks
G. Fazio, H. Aldwinckle, T. Robinson

2. Introduction
Breeding work for the Geneva® rootstocks was
initiated by Drs. Cummins and Aldwinckle in 1967.
The USDA/Cornell program is actively breeding
and selecting new rootstocks (about 2,500 in the
pipeline) – Dr. Aldwinckle and Dr. Robinson
represent Cornell University in the program.
The program, has always focused on developing
yield efficient, disease resistant rootstocks (fire
blight, etc).
It is now focusing on characterization of other
important traits such as replant disease resistance,
drought tolerance, cold tolerance, etc.

3. Apple Harvest Doud family
farm (1916, Miami Co. Indiana)

4. Auvil Fruit Farm (Vantage, WA
2005 – next to Columbia River)

5. Benefits from the
implementation of
dwarfing rootstocks
Less sprays
Less ladder
accidents
Increased productivity

6. Improving Rootstocks for
Superior Tree Performance
Fruit Color and Quality
Fruit Size
Disease Resistance
Plant Architecture – Dwarfing
Molecular mapping and selection tools
Genomics
Yield and productivity (Nutrition)
Precocity
Abiotic Stress Resistance (Cold)
Disease Resistance
Fire blight ($40M 2000 epidemic, MI)
Replant disease complex
TRANSGENIC ROOTSTOCKS for a plethora
of traits

7. Active Apple Rootstock Breeding
Programs 1970s and 80s
Quebec
Malling
Sweden
Norway
Russia
Vineland
Poland
Japan
Michigan
Geneva
Germany
Czech

8. Active Apple Rootstock Breeding
Programs 2005
Russia
S. Korea
Japan
China
Geneva
New Zealand

9. New and Experimental Apple
Rootstocks in the U.S.
Polish
Czhec
Malling
Russia
Vineland
Quebec
Japan
Germany
Geneva
P.14
JTE-B
AR-86-1-20
Bud 57-195
V.1
SJP84-5218
JM1
Supp. 1
G.11
P.22
JTE-C
AR-86-1-25
Bud 60-160
V.2
SJP84-5217
JM2
Supp. 2
G.16
JTE-D
AR-295-6
Bud 61-31
V.3
SJP84-5198
JM3
Supp. 3
G.41
AR-931-15
Bud 62-396
V.4
SJP84-5162
JM7
Supp. 4
G.65
AR-440-1
Bud 64-194
V.7
SJP84-5231
Marubakaido
PiAu 56-83
G.935
AR-680-2
Bud 65-838
SJP84-5174
G.30
AR-486-1
Bud 67-5(32)
SJP84-5189
CG.2001
AR-628-2
Bud 70-8-8
SJP84-5180
CG.2003
AR-69-7
Bud 70-20-21
CG.2006
AR-360-19
Bud 71-3-150
CG.2022
M.20
Bud 71-7-22
CG.2034
CG.2406
CG.3142
CG.3736
CG.3902
CG.4001
CG.4002
CG.4003
CG.4004
CG.4005
CG.3001
CG.4011
CG.4013
CG.4018
CG.4019
CG.4021
CG.4038
CG.4049
CG.4088
CG.3007
CG.4094
CG.4113
CG.4172
CG.4210
CG.4213
CG.4214
CG.4247
CG.4288
CG.3029

10. Geneva Rootstock Selection Traits
TRAIT
Fire Blight resistance
Phytopthora resistance
Replant Disease Complex
Wholly apple aphid res.
EVALUATION YEARS
1 or 7
1
1 or 7
1
LOCATION
Greenhouse/Field
Greenhouse
Greenhouse/field
Greenhouse
Juvenility - Spines
3-4
Field/Stoolbed
Stoolbed rooting
3-4
Field/Stoolbed
Growth habit - Brittleness
3-4
Field/Stoolbed
Dwarfing
8-12
Orchard
Precocity
8
Orchard
Suckering
8
Orchard
Yield – Biennial bearing
12
Orchard
Cold hardiness
Drought tolerance
Graft union compatibility
15
Orchard
4
Orchard
5
Orchard

11. Insects and diseases of apple
rootstocks
Fire blight (Erwinia amylovora)
Crown rot, root rot (Phytophthora spp.)
Woolly Apple Aphid (Eriosoma lanigerum)
Southern Blight (Sclerotium rolfsii)
White root rot (Rosellinia necatrix)
Texas root rot (Phymatotrichum omnivora)

12. Apple Rootstock Breeding:
Resources and Activities
Orchard Production
Lab & Greenhouse
-Seedling inoculations
-Molecular markers
-Tissue culture
-Plant pathology
-ETC.
-Individual yield and
growth
-Disease incidence
-Scion compatibility
-ETC.
Nursery
-Liner production
-Tree Production
-Stoolbed evaluation
-Transplant Evaluation
-ETC.
Apple Rootstock Breeding is a very resource intensive endeavor.

13. Apple Rootstock Breeding and
Selection Protocols
Stage 1
Stage 2
Stage 3
Stage 4
Stage 5
Stage 6
Stage 7
Stage 8
Stage 9
Stage 10
Years 1-2
Objective 1.1
Years 3-4
Years 5-6
Years 7-12
Years 10-15
Years 16-18
Years 19-21
Years 22-24
Years 25-27
Years 27-30
1. Select elite parents
Critical Juncture: Molecular
information about allelic
constitution at disease resistance
loci and about other important
traits can be used to bypass first
test orchard.
2. Generate F1 populations
3. Stratify and plant populations
4. MAS for dwarfing, precocity,
disease resistance, etc.
5. Disease screening
6. Plant selected stools
Repeated inoculations with
Fireblight, Wooly Apply Aphid,
Phytophtora, Powdery Mildew and
comparison to known standards
7. Stool selection
8. Propagation and grafting
9. First test orchard
10. First test evaluation and selection
11. Elite stoolbed establishment
12. Stress tolerance tests - drought,
cold hardiness, graft union strength
13. Elite liner and tree production
14. Elite stoolbed selection and
distribution to nurseries
15. Intermediate replicated orchard
16. Intermediate orchard evaluation
17. Commercial stoolbed evaluation
18. NC-140 and cooperator trials
(national and international)
19. Commercial production ramp up
Patent and UPOV protection
20. Comercial sale
Contingent on goodness of MAS
Highly replicated first test orchard
at multiple sites
Test orchard Evaluation and Selection
Elite stoolbed establishment
Stress tolerance tests - drought,
cold hardiness, graft union strength
Elite stoolbed selection and
distribution to nurseries
Commercial stoolbed evaluation and
distribution of trees to trial sites
NC140 and cooperator trials
(national and internationa)
Commercial production ramp up
Commercial sale
Feedback from
Horticultural Traits
evaluations, disease
resistance evaluations,
stress tolerance
evaluationswill be
combined with molecular
data and used in
subsequent cycles of
selection. Elite material
from these evaluations
are used as parents in
subsequent cycles.
These Stress Tolerance Tests
willl have to be highly replicated
at each location - therefore only
a few selections at a time will
be tested. Grower cooperators
in cold or drought prone areas
in the US will be selected for
cold hardiness and drought
stress. For graft union
compatibility and strength a set
of rootstocks will be grafted
with multiple scions and graft
unions tested after 3 years.

14. Breeding and Selection of
Apple Rootstocks - Simplified
10,000
Number of
genotypes
observed
Number of
replications
per genotype
Number of plants
1000
Transgenic
“value-added”
traits
100
10
1
1
2
3
4
5
6
7
8
Time (3 year stages)
9
10
B. Johnson

15. Criteria for Parent Selection –
Phenotype and Molecular Markers
Dwarfing
Precocity
Disease Resistance
Fire Blight
AD13 SCAR scab marker (Boudichevskaia et al. 2006)
Phytopthora
Powdery Mildew
Apple Scab
Yield and Field
Performance
“New” Gene Pools
EM M01 SCAR powdery mildew marker (Evans et al. 2003)

16. New Gene Pools at the Plant
Genetic Resources Unit (PGRU)
Geneva, New York
Malus - Apple - 3995
accessions 2430
clones (grafted) and
1565 seedlots from
wild
2808 wild Malus
seedlings from
310 populations
from
Kazakhstan,
Russia, China &
Turkey

17. Malus sieversii from Kazakhstan 1989 - 1996
Site 9 w/ depletion by grazing animals
Excellent apple-scab resistance from some sites
Site 5
Site 6

18. Gene Pool Identification –
Combining SSR, SCAR Markers
MM.111
PiAu5683
M.2
MM.106
M.13 P.14
M.1 M.7P.18PiAu5111
J-TE-C V.1
M.27
M.11
G.65
M.10
M?
M.3
0.81
G.41
0.14
G.202
J.9
Pi80
M.9T337
B.118 PiAu514
M.9
M.26
J-TE-G
M.8
M.20
M.25
V.7
V.2
G.11 G.30
G3007
G.935
G5179
R.5
III
III
Alnarp
M.4
O.3
B.9
P.1
B.491
JM.10
-0.52
-0.52
1.00
0.47
0.47
-1.19
II -0.06
G.16
Novole
Maruba
NAGA
-0.59
-1.11
-1.86
-1.86
-1.03
-0.59
-0.15
I
0.29
0.29
G3007
G.935
O.3
G5179
G.202
G.30
G.11
B.9
M.8
M.20
J.9
JM.10
J-TE-G
Pi80
M.9
M.9T337
V.2
M?
P.1
P.14
G.16
V.1
G.41
M.27
G.65
PiAu5111MW
M.10
M.13
M.26
Alnarp
PiAu514
M.1
M.2
M.4
M.11
M.3
PiAu5683
M.7
PiAu5111
P.18
R.5
V.7
J-TE-C
M.25
MM.106
MM.111
B.491
B.118
Maruba
NAGA
Novole
0.00
0.72
0.21
0.42
Coefficient
0.63
0.83

19. Crossing Parents – Stage 1

20. Crossing Parents – Stage 1

21. Seed Harvest – Stage 1 –
2,000-10,000 seeds per cross

22. Disease Screens – Stage 1 –
3,000 to 10,000 seedlings/year

23. Disease Screens – Stage 1 –
3,000 to 10,000 seedlings/year

24. Fire blight - Erwinia amylovora
Major disease for apple rootstocks in North
America
Bacterial disease with strain differentiation
Resistance sources available
Rootstock infection routes:
suckers
injuries
systemic movement of bacteria from scion

25. Fire Blight Screening – Stage 1
500 to 2,000 seedlings

26. Integration of Marker Assisted
Selection – Stage 2
High throughput
PCR markers –
SCARs, SSRs
Target traits:
Dwarfing
Powdery mildew
resistance
Scab resistance
Wooly apple aphid
resistance
Use published and
“in house”
markers

27. Propagation and Evaluation of
Layering Stool-Bed Properties

28. Harvest of Rootstock Liners –
Evaluation of Rooting

29. Rootstock Liners in Tree
Nursery for Budding/Grafting

30. First Test Orchard – Stage 3
3-10 replicates per
rootstock genotype
50-100 different
genotype selections
every year
All grafted with same
scion
Evaluated for 8-12
years

31. Early field selection of precocious
genotypes – Stage 4

32. Expansion of Layering Beds to
Increase Replications – Stage 4

33. Evaluation of Layering Stool
Beds – Stage 5

34. Rootstock Liner Evaluation –
Stage 5

35. Second Test for Resistance to
Biotic Stresses – Stage 5
Inoculation with
Wooly Apple
Aphid (Eriosoma
lanigerum)
Water Logging
test with
Phytophthora
Inoculation
Fire Blight Inoculations with
Multiple Strains

36. Replicated Orchard Trials in
Multiple Locations – Stage 6
Precocity
Yield
Fruit Size
Dwarfing
Tree Survival
Disease Incidence
Tree Architecture
Burr Knots

37. Cumulative Yield Efficiency
Measurements
Descriptive Statistics
M.9
Variable: CUM-YEFF
Anderson-Darling Normality Test
A-Squared:
P-Value:
0.5
2.0
3.5
5.0
17.106
0.000
8.0
95% Confidence Interval for Mu
2.59040
1.19212
1.42114
1.75248
3.70960
317
Minimum
1st Quartile
Median
3rd Quartile
Maximum
6.5
Mean
StDev
Variance
Skewness
Kurtosis
N
0.24800
1.87200
2.20500
2.91550
8.18500
95% Confidence Interval for Mu
2.45867
2.08
2.18
2.28
2.38
2.48
2.58
2.68
2.78
2.72214
95% Confidence Interval for Sigma
1.10598
1.29292
95% Confidence Interval for Median
95% Confidence Interval for Median
2.13806
2.34268

38. Replicated Orchard Trials in
Multiple Locations – Stage 6
Descriptive Statistics
Variable: Suckers
Anderson-Darling Normality Test
A-Squared:
P-Value:
10
40
70
100
130
160
95% Confidence Interval for Mu
Mean
StDev
Variance
Skewness
Kurtosis
N
21.1430
29.4424
866.858
2.55072
8.75868
317
Minimum
1st Quartile
Median
3rd Quartile
Maximum
190
27.087
0.000
0.000
2.000
9.500
29.166
204.000
95% Confidence Interval for Mu
17.889
5
15
25
24.397
95% Confidence Interval for Sigma
27.315
31.932
95% Confidence Interval for Median
95% Confidence Interval for Median
6.719
13.403

39. Timing of fire blight screens
Number of
genotypes
observed
Number of
replications
per genotype
9
Rootstock blight
orchard trials
Number of plants
1
Transgene
mediated
resistance
Strain specific
direct inoculation
5
screens
1
2
Time

40. Screening for Resistance to Fire
Blight (E. amylovora)
FIELD INOCULATIONS
ON FINISHED TREES
GREENHOUSE
INOCULATIONS
ON LINERS

41. Commercial Stool Bed Trials –
Stage 7
On site trials of elite rootstocks at commercial nursery locations
Evaluate liner productivity and quality under commercial
conditions
Generates nursery stock for major orchard trials (NC-140, large
grower trials)

42. Program Protocol
Trials with NC-140 Cooperators –
Stage 8

43. Drought Tolerance Tests
Work of Dr. PARRA

44. Graft Union Strength Tests
Pictures Courtesy of Mike Parker (NC State University)

45. On Farm and Nursery Trials in
Several U.S. Locations – Stage 9
Large scale trials planted in WA, PA, MI, NY
Trials include 20-45 different genotypes

46. Nursery Tree Measurements
on 10-15 Trees per Rootstocks
Branch Length
Tree Height
Branch Angle
0=Flat
90=Upright
Total Number of
Branches
Branch Height

47. Branch Angles of Brookfield Gala Trees on Several
Dwarfing Rootstocks for 7 W hirls
Branch Angle (0=Flat 90=Upright)
60
2034
2406
3041
50
40
4210
4213
4214
4814
5935
B9
G11
30
20
10
0
1
2
3
4
Whirl (3 branches)
5
6
7
G16
G?
M9

48. Stages of Micro-Propagation
Prior to Release – Stage 10

49. Commercial Release and
Continued Testing – Stage 10
Program has released 6 new rootstock
genotypes to date.
G.16 and G.30 G.202, G.41, G.935, G.11
are commercially available in U.S.
Release decision for six more elite rootstock
genotypes expected in 2008.

50. Large Scale Production of
Rootstock Liners

51. Production of High Quality Nursery
Trees and Adoption By Growers
Nursery trees on Geneva 202 rootstocks and planted in high density orchard.

52. QTL Mapping of Apple Rootstock
Yield & Disease Resistance Traits
F2
0.0
1.5
2.6
3.7
4.8
7.7
12.0
CH02f06
E32M41-0208
E31M41-0089
G15-1250
CH02c02a
E35M41-3500
E35M37-0318
15.4
17.0
E35M41-0193
E35M32-0272
22.5
23.5
E35M42-0282
E33M36-0192
1.20
Sieversii596280 Sieversii596283
Orientalis594101
PI594103 Sieversii596282
6589
Pi-Au56-83
NAGA
Kansuenesis59409 AR486-1
Maruba M8
Asiatica594009 WijcikMacP18
Novole AR295-6
ReinetteSim
Seiboldii594094 B9 YellowTrans
J9
AR628-2 P1
Fusca589975
Pi-Au51-4
M26
Fusca589941EsopusSpitzenJM7 5046
NSpy Pi-Au51-11 J-TE-G
B118 J-TE-CM27CrimsonBeauty
P14
Tschonoskii58939
GoldenDel M7 JM4 V1
MM111 Supp4
Orientalis590015 M9 P22
NAKB337
B491
MM106 V2
G65
G16
Toringoides58939
Transitoria58942
6006G30
Transitoria58938
7707
5257179
4213
5030 54214
4013
4210 5935
6143
Ioensis590015
6210
50126874
5757
5087
3041
6969
6879
5890
Angustifolia5897
4814
G11 6253
3007
GH589882
4202
0.85
II
0.21
0.55
III
-0.10
44.8
46.4
47.4
48.1
48.7
49.5
50.3
52.3
53.5
63.3
65.7
66.8
67.7
75.3
AD04-450
CH02c06 AA12-2200
E35M35-0178 E35M32-0460
E36M41-0590
CH03d10 E35M41-1000
E35M35-1500 E32M41-0650
CH02b10 C10-750
CH02a04y
K13-350
E37M32-0113 E33M37-0172
E33M36-0194
CH05e03 E37M36-0195
CH03d01
NZ03c01z
P14-750
E32M42-0340
F05-1500
-0.75
-1.05
-1.69
-1.40
-1.53
-0.42
Coronaria589976
Nertchinsk R5
-0.87
I -0.21
0.45
1.11
Dr. Wan Yizhen
Construct a molecular map of
Apple Rootstock using
microsatellites, SNP, SCAR.
Map and develop markers for
plant architecture and disease
resistance traits.
Develop basic knowledge on
Chinese apomictic species for
seed propagated rootstocks.
Transgenic approaches for
improving rootstock performance.

53. Research Work on Apple
Rootstocks Requires Many
Collaborators and Institutions
Cornell University:
T. Robinson (Orchard Systems)
I. Merwin (Horticulture - Replant)
H. Aldwinckle (Plant Pathology)
L. Cheng (Physiology)
S. Brown (Scion Breeding)
Michigan State University:
R. Perry (Rootstocks)
S. VanNocker (Genomics)
Washington State University:
B. Barrit (Scion Breeding)
D. Main (BioInformatics)
USDA ARS PGRU:
A. Baldo (BioInformatics)
P. Forsline (Apple Collection)
USDA ARS AFRS
Kearneysville:
J. Norelli (Transgenics)
C. Bassett (Stress Physiology)
USDA ARS Wenatchee:
M. Mazzola (Plant Pathology)
Y. Zhu (Genomics)
PENN State University:
T. McNellis (Genomics)
J. Schupp (Horticulture)
Over 40 scientists as NC-140
collaborators
Washington Tree Fruit
Research Commission

54. BASIC SCIENCE
Genomics, Proteomics
Gene Discovery, Expression
Physiology
APPLIED SCIENCE
Plant Breeding
Genetic Transformation
VERY APPLIED SCIENCE
Horticultural Trait Evaluation
Widespread Field Performance
Field Recommendations
NC-140
INDUSTRY, GROWERS, PROCESSORS, CONSUMERS

55. Genomic Revolution
We know that M.7 rootstock is less precocious than
M.9. Do we know why?
We know that M.9 dwarfs more than M.26? Do we
know why?
Through Genomics much is being discovered about
how rootstocks do all that they do.
NSF funded project that aims to discover what genes are
turned on and off in the apple scion by different rootstocks.
(Dr. McNellis, Penn State)
Tree architecture modified by apple rootstocks….
Wealth of new genetic material

56. The Geneva® Apple Rootstock
Breeding Program
THANK YOU
Todd Holleran, Sarah Bauer, Yizhen Wan
Funding from IDFTA, WTFRC, USDA, Cornell

57. The Road Ahead (2003 NC-140
Mtgs. Door County, Wisconsin)